[Fis] Is there a boundary between genetic informatics and genetics?

[Sungchul Ji]

Hi Xueshan and FISers,


Thanks for your generous comments.


(1)  You are probably right that  "Genetics is an information science, the first and most fully developed information science." It seems to be more real.


(2)  In Sung’s statement, imitating human linguistics of letters, words, sentences, texts, he divided the substrate or the media that carry genetic information into the following categories:


                           1                                           2                                        3
A. C, G, T or U → genes/mRNA/proteins → metabolic pathways → functional networks of metabolic pathways

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. . .  Our bewilderment is: Is there a boundary between genetic informatics and genetics?


This is a million dollar question, as they say.  There can be more than one answers to this fundamental question depending on the perspective of the answerer.  My answer, based on the above  scheme or network (modified from the original one by adding the backward U-shaped arrow and four numbers, all in black) would be as follows:


   (i) The network is the complementary union of two aspects -- the formal and the material.  The study of the formal aspect of the network may be identified as an example of "informatics" and the study of the material aspect as "genetics" (which can be divided into molecular or microscopic genetics and macroscopic or classical genetics).

   (ii) The network has 4 nodes and 4 arrows, each of these 8 items or any combinations of them  can be studied as a specialized discipline, including the study of all of the items simultaneously, as I attempted to do in my 11/27/2017 post to this list. I regard such a comprehensive (and ambitious) discipline as a part of what I came to refer to as "gnergetics", or the study ("-tics") of information ("gn-") and energy ("erg-") around 1985 [1].   In contrast,  the work of Petoukhov is primarily concerned with the mathematical underpinning of the molecular genetic structures which he has identified with tensor products of matrices [2].
   (iii) Based on the above considerations, my answer to the above question would two fold:

(a) There is no clear boundary in principle between genetic informatics and genetics.

(b) It may be convenient to distinguish between molecular genetics and  classical genetics, the former being more closely related to informatics and the latter to genetics.


All the best.


Sung




References:
   [1] Ji, S. (2012).  Complementarity.<http://www.conformon.net/wp-content/uploads/2012/08/Excerpts_Chapters_2_complementarity_08192012.pdf>  In: Molecular Theory of the Living Cell: Concepts, Molecular Mechanisms, and Biomedical Applications.  Springer, New York.  Section 2.3, pp. 24-50.  PDF at http://www.conformon.net/wp-content/uploads/2012/08/Excerpts_Chapters_2_complementarity_08192012.pdf
   [2]  See Ref. [12] in my 11/27/2017 post.
<http://www.conformon.net/wp-content/uploads/2012/08/Excerpts_Chapters_2_complementarity_08192012.pdf>


________________________________
From: Fis <fis-bounces at listas.unizar.es> on behalf of Xueshan Yan <yxs at pku.edu.cn>
Sent: Wednesday, December 6, 2017 10:28 AM
To: FIS Group
Subject: [Fis] Is there a boundary between genetic informatics and genetics?


Dear FIS Colleagues:

Last week, Sung and I discussed the problem of information in cell language and human language. Pedro gave his opinion too. I think the Sung’s work is very important to our information science study.

Biology is an informational science, this is the view of Leroy E. Hood of the Nobel prize<http://7769domain.com/Ad/GoIEx2/?token=UCtsZ3V4WVZ6RE05RmxhcGZMOFpraEVaWDQzOUJ4TkwzY0FSQUZtWjMyZHZocEhHakUvakVXeG43RWczeXo1aDlURlg3bFZFR3FHeHBtWm92bkZYT1JpQ2Z4NVhJQ0JodEo5UlJkMUxnNWNjMWs2a21WSTNWak12TlRZSi9Wd25KWG5rMldNUnZQTHJOS0F4OFpWdy9JaTFqVHhveC9aQU1Lc0pHN1RiOU1ZPQ2> winner of 2002. As to this argument, he didn't give a complete biological argument — only a genomics one. Review the history of those disciplines that claimed to be the member of information science in the past years, although we cannot wholly agree with them, for example, Bradley Efron — the former president of the American Statistical Association — thought: "Statistics is an information science, the first and most fully developed information science." But I believe, imitating the Efron's statement: "Genetics is an information science, the first and most fully developed information science." It seems to be more real.

In Sung’s statement, imitating human linguistics of letters, words, sentences, texts, he divided the substrate or the media that carry genetic information into the following categories: A. C, G, T or U → genes/mRNA/proteins → metabolic pathways → functional networks of metabolic pathways, as long as we remember those biological experts — the Nobel prize winner in physiology or medicine in 2013 — whose works are only about the chemical signal (information?) in neurotransmitters, they found that signals from one nerve cell to another must be in the form of small packages of vesicles. In some degree, we are immediately aware of its great significance of the study about hierarchical structure of the substrate or the media which carry genetic information here. But, the final verdict may be made by the biologists rather than our information scientists, that is to say, the right of speech may not be in us. Our bewilderment is: Is there a boundary between genetic informatics and genetics? If so, where is it?

For us, if we want to make information science a success, the understanding of information transmission theory in genetics is indispensable. There is no fugitive and cloistered road to the freedom of information science, depression and desolation absolutely is not a positive information to FIS.



Best wishes,

Xueshan

Peking University
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